Skip to content
New issue

Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community.

Sign up for GitHub

By clicking “Sign up for GitHub”, you agree to our terms of service and privacy statement. We’ll occasionally send you account related emails.

Already on GitHub? Sign in to your account

Jump to bottom

add module for btyper3 #3817

Open
wants to merge 5 commits into
base: master
Choose a base branch
from
Open

add module for btyper3 #3817

wants to merge 5 commits into from

Conversation

rpetit3
Copy link
Contributor

@rpetit3 rpetit3 commented Sep 7, 2023 •
edited

PR checklist

Closes #3816

  • This comment contains a description of changes (with reason).
  • If you've fixed a bug or added code that should be tested, add tests!
  • If you've added a new tool - have you followed the module conventions in the contribution docs
  • If necessary, include test data in your PR.
  • Remove all TODO statements.
  • Emit the versions.yml file.
  • Follow the naming conventions.
  • Follow the parameters requirements.
  • Follow the input/output options guidelines.
  • Add a resource label
  • Use BioConda and BioContainers if possible to fulfil software requirements.
  • Ensure that the test works with either Docker / Singularity. Conda CI tests can be quite flaky:
    • PROFILE=docker pytest --tag <MODULE> --symlink --keep-workflow-wd --git-aware
    • PROFILE=singularity pytest --tag <MODULE> --symlink --keep-workflow-wd --git-aware
    • PROFILE=conda pytest --tag <MODULE> --symlink --keep-workflow-wd --git-aware

@rpetit3 rpetit3 added the new module Adding a new module label Sep 7, 2023
nvnieuwk
nvnieuwk reviewed Sep 12, 2023
View reviewed changes
Copy link
Contributor

@nvnieuwk nvnieuwk left a comment

Choose a reason for hiding this comment

The reason will be displayed to describe this comment to others. Learn more.

Some small comments :p

modules/nf-core/btyper3/main.nf Show resolved Hide resolved
tests/modules/nf-core/btyper3/main.nf Outdated
Copy link
Contributor

Choose a reason for hiding this comment

The reason will be displayed to describe this comment to others. Learn more.

Can you also add a test with a gzipped fasta file?

@edmundmiller edmundmiller requested a review from a team as a code owner October 19, 2023 16:26
@edmundmiller edmundmiller self-requested a review October 19, 2023 16:26
@edmundmiller edmundmiller removed their request for review February 6, 2024 15:34
Sign up for free to join this conversation on GitHub. Already have an account? Sign in to comment
Reviewers

@nvnieuwk nvnieuwk nvnieuwk left review comments

At least 1 approving review is required to merge this pull request.

Assignees
No one assigned
Labels
new module Adding a new module
Projects
None yet
Milestone
No milestone
Development

Successfully merging this pull request may close these issues.

new module: Btyper3
3 participants
@rpetit3 @nvnieuwk @SPPearce